RAB4B-EGLN2 Gene
protein-coding GIFtS : 29 GCID: GC19 P041307
RAB4B-EGLN2 readthrough (non-protein coding)
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Aliasesfor RAB4B-EGLN2 gene
(According to
1 HGNC ,
2 Entrez Gene ,
3 UniProtKB/Swiss-Prot ,
4 UniProtKB/TrEMBL , 5 OMIM , 6 GeneLoc ,
7 Ensembl ,
8 DME ,
9 miRBase ,
and/or 10 fRNAdb )About This Section Subcategory (RNA class): miscRNAQuality score for the clustered with this gene is 3 Aliases RAB4B-EGLN2 Readthrough (Non-Protein Coding) 1 2 PHD13 RERT-LncRNA1 Estrogen-Induced Tag 63 EC 1.14.11.293 HIF-Prolyl Hydroxylase 13 EIT63 Hypoxia-Inducible Factor Prolyl Hydroxylase 13 HIF-PH13 Prolyl Hydroxylase Domain-Containing Protein 13 HPH-13 EC 1.14.118 HPH-33
Export aliases for RAB4B-EGLN2 gene to outside databases Previous GC identifer: GC19U901528
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Summariesfor RAB4B-EGLN2 gene (According to Entrez Gene ,
Tocris Bioscience ,
Wikipedia's
Gene Wiki ,
PharmGKB ,UniProtKB/Swiss-Prot ,
and/or
UniProtKB/TrEMBL )
About This Section Entrez Gene summary for RAB4B-EGLN2 : This locus represents naturally occurring read-through transcription between the neighboring RAB4B (RAB4B, member RAS oncogene family) and EGLN2 (egl nine homolog 2) genes on chromosome 19. The read-through transcript is a candidate for nonsense-mediated mRNA decay (NMD), and is thus unlikely to produce a protein product. (provided by RefSeq, Feb 2011) UniProtKB/Swiss-Prot: EGLN2_HUMAN, Q96KS0 Function : Cellular oxygen sensor that catalyzes, under normoxic conditions, the post-translational formation of4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins. Hydroxylates a specific proline found in each of the oxygen-dependent degradation (ODD) domains (N-terminal, NODD, and C-terminal, CODD) of HIF1A. Also hydroxylates HIF2A. Has a preference for the CODD site for both HIF1A and HIF2A. Hydroxylated HIFs are then targeted for proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Under hypoxic conditions, the hydroxylation reaction is attenuated allowing HIFs to escape degradation resulting in their translocation to the nucleus, heterodimerization with HIF1B, and increased expression of hypoxy-inducible genes. EGLN2 is involved in regulating hypoxia tolerance and apoptosis in cardiac and skeletal muscle. Also regulates susceptibility to normoxic oxidative neuronal death
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Genomic Viewsfor RAB4B-EGLN2 gene
(According to
GeneLoc and/or
HGNC , and/or
Entrez Gene (NCBI build 37) ,miRBase ,UCSC (hg19) and
Ensembl (release 69) ,
Regulatory elements and Epigenetics data according to
QIAGEN ,
SABiosciences , and/or
SwitchGear Genomics )About This Section Regulatory elements: Search SABiosciences Regulatory transcription factor binding sites for RAB4B-EGLN2 Other transcription factors Search SABiosciences Chromatin IP Primers for RAB4B-EGLN2 Epigenetics: QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RAB4B-EGLN2
Genomic Location: Genomic View : UCSC Golden Path with GeneCards custom track Entrez Gene cytogenetic band: 19q Ensembl cytogenetic band: 19q13.2 HGNC cytogenetic band: 19q13.2 RAB4B-EGLN2 Gene in genomic location: bands according to Ensembl, locations according to
Entrez Gene Ensembl GeneLoc information about chromosome 19 GeneLoc Exon Structure
GeneLoc location for GC19P041307: view genomic region
(about GC identifiers )
Start: 41,305,048 bp from pter End:
41,314,337 bp from pter
Size: 9,290 bases Orientation:
plus strand
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Proteinsfor RAB4B-EGLN2 gene
(According to
1 UniProtKB ,
HORDE ,
neXtProt ,
Ensembl ,
and/or Reactome ,
Modification sites according to 2 PhosphoSitePlus ,
Specific Peptides from DME ,
Protein expression images according to data from SPIRE MOPED and PaxDb ,
RefSeq according to NCBI ,
PDB rendering according to OCA and/or Proteopedia ,
Recombinant Proteins
from
EMD Millipore ,
R&D Systems ,
GenScript ,
Enzo Life Sciences ,
OriGene ,
Novus Biologicals ,
Sino Biological ,
ProSpec , and/or
Uscn ,
EMD Millipore ,
R&D Systems ,
OriGene ,
GenScript ,
Cell Signaling Technology ,
Enzo Life Sciences , and/or
Uscn ,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene ,
Antibodies by
EMD Millipore ,
R&D Systems ,
GenScript ,
Cell Signaling Technology ,
OriGene ,
Novus Biologicals ,
Thermo Fisher Scientific ,
Abcam , and/or
Uscn )
About This Section UniProtKB/Swiss-Prot: EGLN2_HUMAN, Q96KS0 See
protein sequence )Recommended Name: Size : 407 amino acids; 43650 DaCofactor : Binds 1 Fe(2+) ion per subunitCofactor : AscorbateSubunit : Interacts (preferably isoform p40) with SIAH2; the interaction targets both SIAH2 isoforms for proteasomaldegradation in vitro. Interacts with LIMD1, WTIP and AJUBA
Subcellular location : NucleusSequence caution : Sequence=AAH01723.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;Secondary accessions : A8K5S0 Q8WWY4 Q9BV14Alternative initiation : 2 isoforms : Q96KS0-1 Q96KS0-2 Explore the universe of human proteins at neXtProt for RAB4B-EGLN2: NX_Q96KS0 Post-translational modifications:
View modification sites using PhosphoSitePlus 2 View neXtProt modification sites for NX_Q96KS0 4 DME Specific Peptides for RAB4B-EGLN2 (Q96KS0 ) RAB4B-EGLN2 Protein expression data from MOPED and PaxDb : About this image ENSEMBL proteins: ENSP00000307080 ENSP00000385253 Reactome Protein details: Q96KS0 Human Recombinant Protein Products: Gene Ontology (GO): 1 cellular component term (GO ID links to tree view) : About this table
GO ID Qualified GO term Evidence PubMed IDs GO:0005634 nucleus
-- --
About GeneDecksing RAB4B-EGLN2 Antibody Products: Assay Products for RAB4B-EGLN2:
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Protein
Domains /for RAB4B-EGLN2 gene (According to InterPro , ProtoNet ,
UniProtKB , and/or BLOCKS ,
Sets of similar genes according to GeneDecks )
About This Section About GeneDecksing 2 InterPro domains/families :
Graphical View of Domain Structure for InterPro Entry Q96KS0 ProtoNet protein and cluster: Q96KS0
UniProtKB/Swiss-Prot: EGLN2_HUMAN, Q96KS0 Domain : The Beta(2)beta(3) 'finger-like' loop domain is important for substrate (HIFs' CODD/NODD) selectivity (Bysimilarity) Similarity : Contains 1 Fe2OG dioxygenase domain
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Functionfor RAB4B-EGLN2 gene
(According to 1 UniProtKB ,
Genatlas ,
LifeMap Discovery™ ,
IUBMB , and/or
2 DME ,
Human phenotypes from GenomeRNAi ,
Animal models from MGI Mar 06 2013,
SABiosciences ,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene ,
RNAi from
EMD Millipore ,
siRNAs from
OriGene ,
QIAGEN ,
microRNA from QIAGEN ,
Gene Editing from DNA2.0 ,
Clones from EMD Millipore ,
OriGene ,
SwitchGear Genomics ,
GenScript ,
Sino Biological ,
DNA2.0 ,
and Vector BioLabs ,
Cell Lines from GenScript ,
LifeMap BioReagents ,
In Situ Hybridization Assays from Advanced Cell Diagnostics ,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene .)
About This Section Function Summary: UniProtKB/Swiss-Prot: EGLN2_HUMAN, Q96KS0 Function : Cellular oxygen sensor that catalyzes, under normoxic conditions, the post-translational formation of4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins. Hydroxylates a specific proline found in each of the oxygen-dependent degradation (ODD) domains (N-terminal, NODD, and C-terminal, CODD) of HIF1A. Also hydroxylates HIF2A. Has a preference for the CODD site for both HIF1A and HIF2A. Hydroxylated HIFs are then targeted for proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Under hypoxic conditions, the hydroxylation reaction is attenuated allowing HIFs to escape degradation resulting in their translocation to the nucleus, heterodimerization with HIF1B, and increased expression of hypoxy-inducible genes. EGLN2 is involved in regulating hypoxia tolerance and apoptosis in cardiac and skeletal muscle. Also regulates susceptibility to normoxic oxidative neuronal death Catalytic activity : Hypoxia-inducible factor-L-proline + 2-oxoglutarate + O(2) = hypoxia-induciblefactor-trans-4-hydroxy-L-proline + succinate + CO(2) Induction : By estrogen. Isoform p43 is induced by hypoxia leading to protein stability. Isoform p40 repressed byhypoxia. Both isoforms are induced by proteasomal inhibitor MG132 (at protein level) Enzyme Numbers (IUBMB): EC 1.14.11 2 EC 1.14.11.29 1
In Situ AssayAdvanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAB4B-EGLN2
Gene Ontology (GO): 5/7 molecular function terms (GO ID links to tree view) (see all 7 ): About this table
GO ID Qualified GO term Evidence PubMed IDs GO:0005515 protein binding
-- -- GO:0008198 ferrous iron binding
-- -- GO:0016491 oxidoreductase activity
-- -- GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
-- -- GO:0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors
-- --
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Pathways & Interactionsfor RAB4B-EGLN2 gene
(Pathways according to
EMD Millipore ,
R&D Systems ,
Cell Signaling Technology ,
KEGG ,
PharmGKB ,
BioSystems ,
Reactome ,
Tocris Bioscience ,
GeneGo (Thomson Reuters) ,
QIAGEN ,
and/or UniProtKB ,
Sets of similar genes according to GeneDecks ,
Interaction Networks according to
SABiosciences ,
and/or STRING ,
Interactions according to 1 UniProtKB ,
2 MINT ,
3 I2D , and/or
4 STRING ,
with links to IntAct and
Ensembl ,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene) .
About This Section Pathway sources See GeneCards unified pathways Show all pathways 4 About GeneDecksing Interactions: Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RAB4B-EGLN2 STRING Interaction
Network Preview (showing 5 interactants - click image to see 21)5/24 Interacting proteins for RAB4B-EGLN2 (Q96KS0 2 , 3 ENSP00000307080 4 via UniProtKB, MINT, STRING , and/or I2D (see all 24 )About this table Gene Ontology (GO): 5/7 biological process terms (GO ID links to tree view) (see all 7 ): About this table
GO ID Qualified GO term Evidence PubMed IDs GO:0001558 regulation of cell growth
-- -- GO:0001666 response to hypoxia
-- -- GO:0030520 intracellular estrogen receptor signaling pathway
-- -- GO:0043523 regulation of neuron apoptotic process
-- -- GO:0045454 cell redox homeostasis
-- --
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Drugs & Compoundsfor RAB4B-EGLN2 gene (Chemical Compounds according to UniProtKB , Enzo Life Sciences ,
EMD Millipore , Tocris Bioscience
HMDB ,
BitterDB , and/or
Novoseek , and Drugs according to
DrugBank ,
Enzo Life Sciences , and/or
PharmGKB , with drugs/clinical trials/news
search links to CenterWatch )
About This Section Browse Tocris compounds for RAB4B-EGLN2 RAB4B-EGLN2 / EGLN2
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Transcriptsfor RAB4B-EGLN2 gene (Secondary structures according to
fRNAdb ,Unigene
(Build 235 Homo sapiens; Mar 10 2013) or GenBank , Entrez Gene ,
DOTS (version 10), and/or
AceView ,
transcript ids from Ensembl
with links to UCSC , GeneLoc ,
alternative splicing isoforms according to ASD and/or
ECgene ,EMD Millipore ,
OriGene ,
QIAGEN ,
shRNA from
OriGene ,
microRNA from QIAGEN ,
OriGene ,
SwitchGear Genomics ,
GenScript ,
DNA2.0 ,
Vector BioLabs ,
Primers from
OriGene ,
SABiosciences , and/or
QIAGEN
)About This Section 2 Ensembl transcripts including schematic representations, and UCSC links where relevant : ENST00000303961 (uc002opg.4 ) ENST00000406058 (uc010ehd.3 uc002oph.3 uc002opi.3 )GeneLoc Exon Structure 5/14 Alternative Splicing Database (ASD) splice patterns (SP) for RAB4B-EGLN2 (see all 14 ) About this scheme ExUns: 1 ^ 2a · 2b ^ 3a · 3b · 3c ^ 4 ^ 5a · 5b · 5c · 5d · 5e · 5f · 5g ^ 6 ^ 7a · 7b · 7c ^ 8a · 8b ^ 9 ^ 10a · 10b · 10c · 10d SP1 : - - - - - - - - - - SP2 : - - - - - - - - - SP3 : - - - - SP4 : - - - SP5 : -
ECgene alternative splicing isoforms for RAB4B-EGLN2
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Expression for RAB4B-EGLN2 gene
(RNA expression data according to
H-InvDB ,
NONCODE ,
miRBase , and
RNAdb ,
Expression images according to data from
BioGPS ,
Illumina Human BodyMap , and
CGAP
SAGE ,
Sets of similar genes according to GeneDecks ,
in vivo and in vitro expression data from LifeMap Discovery™ ,
plus additional links to
Genevestigator , and/or
SOURCE , and/or
BioGPS , and/or
UniProtKB ,SABiosciences ,
Primers from
OriGene ,
SABiosciences , and/or
QIAGEN ,
In Situ Hybridization Assays from Advanced Cell Diagnostics )
About This Section See probesets specificity/sensitivity at GeneAnnot CGAP TAG: -- See RAB4B-EGLN2 Protein Expression from SPIRE MOPED and PaxDB UniProtKB/Swiss-Prot: EGLN2_HUMAN, Q96KS0 Tissue specificity : Expressed in adult and fetal heart, brain, liver, lung, skeletal muscle, and kidney. Also expressedin testis and placenta. Highest levels in adult brain, placenta, lung, kidney, and testis. Expressed in hormone responsive tissues, including normal and cancerous mammary, ovarian and prostate epithelium SABiosciences Custom PCR Arrays for RAB4B-EGLN2 Primer Browse OriGene genome-wide validated SYBR primer pairs Browse OriGene validated miRNA SYBR primer pairs Search SABiosciences RT2 qPCR
Primer Assays in human, mouse, rat RAB4B-EGLN2 Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RAB4B-EGLN2 Search QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RAB4B-EGLN2 In Situ Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAB4B-EGLN2
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Orthologsfor RAB4B-EGLN2 gene
(Orthologs according to
1,2 HomoloGene (2 older version, for species not in 1 newer version),
3 euGenes ,
4 SGD
,
5 MGI Mar 06 2013,
with possible further links to
Flybase
and/or
WormBase ,
and/or
6 Ensembl pan taxonomic compara ,
Gene Trees according to Ensembl and
TreeFam )
About This Section Orthologs for RAB4B-EGLN2 gene from 3/14 species (see all 14 ) About this table
Organism
Taxonomic
Gene
Description
Human
Orthology
Details
lizard Reptilia MIA6
--
90(a)
1 → many
LGf(2855521-2864702)
zebrafish Actinopterygii rab4b6
RAB4B, member RAS oncogene family
92(a)
1 → many
15(8949071-8991707)
fruit fly Insecta Rab46
Rab-protein 4
76(a)
1 → many
2R(13460964-13462484)
ENSEMBL Gene Tree for RAB4B-EGLN2 (if available)TreeFam Gene Tree for RAB4B-EGLN2 (if available)
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Paralogsfor RAB4B-EGLN2 gene (Paralogs according to
1 HomoloGene ,2 Ensembl , and 3 SIMAP , Pseudogenes according to 4 Pseudogene.org Build 68)About This Section Paralogs for RAB4B-EGLN2 gene EGLN3 2 EGLN1 2 About GeneDecksing
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Genomic Variantsfor RAB4B-EGLN2 gene (SNPs/Variants according to the
1 NCBI SNP Database ,
2 Ensembl ,
3 PupaSUITE ,
UniProtKB , and
DNA2.0 ,
Linkage Disequilibrium by HapMap ,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants , Mutations from the Human Gene
Mutation Database (HGMD) and the Locus Specific Mutation
Databases (LSDB) , Blood group antigen gene mutations by BGMUT ,
Resequencing Primers from QIAGEN ,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences )
About This Section SABiosciences Cancer Mutation PCR Assays
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Disorders
/ Diseasesfor RAB4B-EGLN2 gene
(in which this Gene is Involved, According to MalaCards ,
OMIM, UniProtKB ,
the University of Copenhagen DISEASES
database ,
Genatlas , GeneTests ,
GAD ,
HuGE Navigator ,
and/or TGDB .)
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Publicationsfor RAB4B-EGLN2 gene (in
PubMed .
Associations of this gene to articles via
1 Entrez Gene ,
2 UniProtKB/Swiss-Prot ,
3 HGNC ,
4 GAD ,
5 PharmGKB ,
6 HMDB ,
7 DrugBank ,
8 UniProtKB/TrEMBL ,
9 Novoseek , and/or
10 fRNAdb )
About This Section PubMed articles for RAB4B-EGLN2 gene, integrated from 9 sources (see all 19 ):(articles sorted by number of sources associating them with RAB4B-EGLN2) Utopia : connect your pdf to the dynamic
An insertion/deletion polymorphism within RERT-lncRNA modulates hepatocellular carcinoma risk. (PubMed id 23026137) 1 , 3(2012) The LIMD1 protein bridges an association between the prolyl hydroxylases and VHL to repress HIF-1 activity. (PubMed id 22286099) 2 (2012) Biochemical characterization of human HIF hydroxylases using HIF protein substrates that contain all three hydroxylation sites. (PubMed id 21410436) 2 (2011) Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PubMed id 20967262) 1 (2010) Role of the intracellular localization of HIF-prolyl hydroxylases. (PubMed id 19339211) 2 (2009) Cellular oxygen sensing: Importins and exportins are mediators of intracellular localisation of prolyl-4-hydroxylases PHD1 and PHD2. (PubMed id 19631610) 2 (2009) The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005) 2 (2007) Characterization of different isoforms of the HIF prolyl hydroxylase PHD1 generated by alternative initiation. (PubMed id 16509823) 2 (2006) Differential function of the prolyl hydroxylases PHD1, PHD2, and PHD3 in the regulation of hypoxia-inducible factor. (PubMed id 15247232) 2 (2004) The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334) 2 (2004)
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External Searches for RAB4B-EGLN2 gene
(in PubMed ,
OMIM , and NCBI Bookshelf ) About This Section
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Genome Databases showing RAB4B-EGLN2 gene
(According to
Entrez Gene ,
HGNC ,
AceView ,
euGenes ,
Ensembl ,
miRBase ,
ECgene ,
Kegg ,
and/or
H-InvDB )
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Other Databases showing RAB4B-EGLN2 gene
(According to HUGE )
About This Section --
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Specialized Databases showing RAB4B-EGLN2 gene (According to PharmGKB ,
ATLAS , HORDE , IMGT , LEIDEN , UniProtKB/Swiss-Prot , and/or UniProtKB/TrEMBL ,Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot )About This Section
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About This Section Patent Information for RAB4B-EGLN2 gene: RAB4B-EGLN2 GeneCards and IP: Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
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Productsfor RAB4B-EGLN2 gene (Antibodies, recombinant proteins, and assays from EMD Millipore , R&D Systems , OriGene , QIAGEN , GenScript , Cell Signaling Technology , SABiosciences , Novus Biologicals , Sino Biological , Enzo Life Sciences , Abcam , ProSpec , Uscn , Thermo Fisher Scientific , Gene Editing from DNA2.0 , Clones from EMD Millipore , OriGene , GenScript , Sino Biological , DNA2.0 , SwitchGear Genomics , Vector BioLabs , Cell lines from GenScript and LifeMap BioReagents , PCR Arrays from SABiosciences , Drugs and/or compounds from EMD Millipore , Tocris Bioscience , and/or
Enzo Life Sciences ), In Situ Hybridization Assays from Advanced Cell Diagnostics About This Section
QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat RAB4B-EGLN2 Search QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RAB4B-EGLN2 QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RAB4B-EGLN2 Search QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat RAB4B-EGLN2 Search QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RAB4B-EGLN2 Search QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RAB4B-EGLN2
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RAB4B-EGLN2
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